Human/hg19/GRCh37 46-way multiple alignment

The 46 species multiple alignment on human/hg19/GRCh37 is an extra large bit of work. A discussion of the phylogenetic trees used in the alignment is included here.

Errata

The initial release of this track include a phylogenetic tree that had two small errors in it. 46way.nh
Namely: Baboon (papHam1) and Rhesus (rheMac2) were specified as separate nodes instead of correctly sister species. The same problem is present for Wallaby (macEug1) and Opossum (monDom5). The discussion below includes a corrected phylogenetic tree.

Corrected Tree

I'm currently rerunning a test with the multiple alignment and phastCons/phyloP annotations to see if the corrected tree makes any significant difference in the result. I'm expecting the difference to be minor. In the meantime, included here is a corrected tree:

(((((((((((((((((
hg19:0.006690,panTro2:0.006663):0.002736,gorGor1:0.008781):0.009574,
ponAbe2:0.018320):0.014347,
(rheMac2:0.007863,papHam1:0.007644):0.029610):0.021965,
calJac1:0.066248):0.057725,tarSyr1:0.138111):0.011068,
(micMur1:0.092694,otoGar1:0.129822):0.035615):0.015654,
tupBel1:0.186600):0.004734,(((((mm9:0.084475,rn4:0.091689):0.198456,
dipOrd1:0.212120):0.022998,cavPor3:0.225832):0.009965,
speTri1:0.148889):0.025869,(oryCun2:0.113952,
ochPri2:0.201056):0.101863):0.015314):0.020677,
(((vicPac1:0.107300,(turTru1:0.064649,bosTau4:0.123608):0.025219):0.040465,
((equCab2:0.109511,(felCat3:0.098624,canFam2:0.102582):0.050027):0.006078,
(myoLuc1:0.142585,pteVam1:0.113375):0.033777):0.004432):0.011563,
(eriEur1:0.222118,sorAra1:0.269476):0.056631):0.021325):0.023667,
(((loxAfr3:0.082207,proCap1:0.155479):0.026990,echTel1:0.246016):0.049975,
(dasNov2:0.116621,choHof1:0.096458):0.053301):0.006623):0.234681,
(monDom5:0.126451,macEug1:0.122582):0.215267):0.074190,
ornAna1:0.453572):0.105220,((galGal3:0.164727,taeGut1:0.171381):0.198499,
anoCar1:0.489779):0.107898):0.188168,xenTro2:0.847575):0.300265,
(((tetNig2:0.223507,fr2:0.203488):0.182455,
(gasAcu1:0.310214,oryLat2:0.480345):0.073203):0.316470,
danRer6:0.731528):0.180826):0.480450,petMar1:0.480450);

Multiple Trees

For the phyloP/phastCons calculations, there are a number of trees that were used.

There is a set of trees with branch lengths calculated based only on the ordinary chromosomes without chrX, and a set of trees calculated based only on chrX.

Within those two categories, there are three trees with branch lengths calculated from subsets of the 46 species:

1. primate subset only
2. placental mammal subset only
3. all 46 vertebrates

Thus, there are six different phylogenetic trees.